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Aliases for VPS9D1 Gene

Aliases for VPS9D1 Gene

  • VPS9 Domain Containing 1 2 3 5
  • C16orf7 3 4
  • Chromosome 16 Open Reading Frame 7 2
  • VPS9 Domain-Containing Protein 1 3
  • Protein ATP-BL 4
  • ATP-BL 3
  • ATPBL 4

External Ids for VPS9D1 Gene

Previous HGNC Symbols for VPS9D1 Gene

  • C16orf7

Previous GeneCards Identifiers for VPS9D1 Gene

  • GC16M089774

Summaries for VPS9D1 Gene

GeneCards Summary for VPS9D1 Gene

VPS9D1 (VPS9 Domain Containing 1) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include GTPase activator activity and transporter activity.

Gene Wiki entry for VPS9D1 Gene

Additional gene information for VPS9D1 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS9D1 Gene

Genomics for VPS9D1 Gene

GeneHancer (GH) Regulatory Elements for VPS9D1 Gene

Promoters and enhancers for VPS9D1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16I089717 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 569.9 +0.2 219 7.5 PKNOX1 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 YY1 POLR2B ZNF766 VPS9D1 ZNF276 AFG3L1P CDK10 LOC101927863 ENSG00000268218 ACSF3 ANKRD11 MC1R TCF25
GH16I089686 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 11.3 +34.0 33961 2.5 PKNOX1 FOXA2 MLX ARID4B SIN3A DMAP1 YY1 SLC30A9 POLR2B ZNF207 CDK10 LINC02166 DPEP1 VPS9D1 ZNF276 FANCA PIR59284
GH16I089832 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 11.8 -114.5 -114527 6.6 CLOCK FOXA2 MLX ZFP64 ARID4B NEUROD1 SIN3A DMAP1 BRCA1 ZNF48 CDK10 SPIRE2 ACSF3 TUBB3 GALNS VPS9D1 ZNF276 ANKRD11 SNORD68 FANCA
GH16I089842 Enhancer 1.3 Ensembl ENCODE dbSUPER 11.8 -121.8 -121830 1.5 NFIB SIN3A ZNF48 RFX5 ZNF335 ZNF121 GLIS2 ZNF366 EGR1 FOS SPATA2L SPIRE2 CDK10 FANCA VPS9D1 ZNF276 LOC105371419
GH16I089763 Enhancer 1 Ensembl ENCODE 12.9 -43.4 -43400 2.9 HDGF PKNOX1 BMI1 BATF IRF4 RAD21 ZNF207 ZNF143 ATF7 ETV6 FANCA CDK10 SPIRE2 VPS9D1 ZNF276 SPATA2L GAS8 PIR55781
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around VPS9D1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for VPS9D1 Gene

Genomic Locations for VPS9D1 Gene
chr16:89,707,133-89,721,272
(GRCh38/hg38)
Size:
14,140 bases
Orientation:
Minus strand
chr16:89,773,541-89,787,394
(GRCh37/hg19)

Genomic View for VPS9D1 Gene

Genes around VPS9D1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VPS9D1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VPS9D1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS9D1 Gene

Proteins for VPS9D1 Gene

  • Protein details for VPS9D1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y2B5-VP9D1_HUMAN
    Recommended name:
    VPS9 domain-containing protein 1
    Protein Accession:
    Q9Y2B5

    Protein attributes for VPS9D1 Gene

    Size:
    631 amino acids
    Molecular mass:
    68956 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA76711.1; Type=Frameshift; Positions=Several; Evidence={ECO:0000305};

    Alternative splice isoforms for VPS9D1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS9D1 Gene

Post-translational modifications for VPS9D1 Gene

No Post-translational modifications

No data available for DME Specific Peptides for VPS9D1 Gene

Domains & Families for VPS9D1 Gene

Gene Families for VPS9D1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for VPS9D1 Gene

Suggested Antigen Peptide Sequences for VPS9D1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with VPS9D1: view

No data available for UniProtKB/Swiss-Prot for VPS9D1 Gene

Function for VPS9D1 Gene

Phenotypes From GWAS Catalog for VPS9D1 Gene

Gene Ontology (GO) - Molecular Function for VPS9D1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005096 GTPase activator activity IEA --
GO:0005215 transporter activity TAS 10231027
genes like me logo Genes that share ontologies with VPS9D1: view
genes like me logo Genes that share phenotypes with VPS9D1: view

Animal Model Products

miRNA for VPS9D1 Gene

miRTarBase miRNAs that target VPS9D1

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for VPS9D1 Gene

Localization for VPS9D1 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VPS9D1 gene
Compartment Confidence
nucleus 3
cytosol 3
mitochondrion 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for VPS9D1 Gene

Pathways & Interactions for VPS9D1 Gene

SuperPathways for VPS9D1 Gene

No Data Available

Interacting Proteins for VPS9D1 Gene

STRING Interaction Network Preview (showing 2 interactants - click image to see details)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000374037%0d%0a9606.ENSP00000417281%0d%0a9606.ENSP00000269305%0d%0a
Selected Interacting proteins: Q9Y2B5-VP9D1_HUMAN ENSP00000374037 for VPS9D1 Gene via IID STRING UniProtKB

Gene Ontology (GO) - Biological Process for VPS9D1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015986 ATP synthesis coupled proton transport TAS 10231027
GO:0043547 positive regulation of GTPase activity IEA --
genes like me logo Genes that share ontologies with VPS9D1: view

No data available for Pathways by source and SIGNOR curated interactions for VPS9D1 Gene

Drugs & Compounds for VPS9D1 Gene

No Compound Related Data Available

Transcripts for VPS9D1 Gene

Unigene Clusters for VPS9D1 Gene

VPS9 domain containing 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for VPS9D1 Gene

No ASD Table

Relevant External Links for VPS9D1 Gene

GeneLoc Exon Structure for
VPS9D1
ECgene alternative splicing isoforms for
VPS9D1

Expression for VPS9D1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VPS9D1 Gene

mRNA differential expression in normal tissues according to GTEx for VPS9D1 Gene

This gene is overexpressed in Whole Blood (x7.3).

Protein differential expression in normal tissues from HIPED for VPS9D1 Gene

This gene is overexpressed in Fetal Brain (31.4), Frontal cortex (26.7), and Retina (10.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for VPS9D1 Gene



Protein tissue co-expression partners for VPS9D1 Gene

NURSA nuclear receptor signaling pathways regulating expression of VPS9D1 Gene:

VPS9D1

SOURCE GeneReport for Unigene cluster for VPS9D1 Gene:

Hs.164410

mRNA Expression by UniProt/SwissProt for VPS9D1 Gene:

Q9Y2B5-VP9D1_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for VPS9D1 Gene

  • Blood(4.1)
genes like me logo Genes that share expression patterns with VPS9D1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for VPS9D1 Gene

Orthologs for VPS9D1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for VPS9D1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VPS9D1 33 34
  • 92.25 (n)
cow
(Bos Taurus)
Mammalia VPS9D1 33 34
  • 83.64 (n)
dog
(Canis familiaris)
Mammalia VPS9D1 33 34
  • 82.78 (n)
mouse
(Mus musculus)
Mammalia Vps9d1 33 16 34
  • 81.34 (n)
rat
(Rattus norvegicus)
Mammalia Vps9d1 33
  • 80.96 (n)
oppossum
(Monodelphis domestica)
Mammalia VPS9D1 34
  • 70 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VPS9D1 34
  • 69 (a)
OneToOne
chicken
(Gallus gallus)
Aves C11H16ORF7 33
  • 68.5 (n)
VPS9D1 34
  • 61 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VPS9D1 34
  • 64 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vps9d1 33
  • 58.08 (n)
Str.15453 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.29400 33
zebrafish
(Danio rerio)
Actinopterygii vps9d1 33 34
  • 60 (n)
idibd5127 33
Species where no ortholog for VPS9D1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for VPS9D1 Gene

ENSEMBL:
Gene Tree for VPS9D1 (if available)
TreeFam:
Gene Tree for VPS9D1 (if available)

Paralogs for VPS9D1 Gene

No data available for Paralogs for VPS9D1 Gene

Variants for VPS9D1 Gene

Sequence variations from dbSNP and Humsavar for VPS9D1 Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs1000156031 -- 89,722,405(-) C/T upstream_transcript_variant
rs1000230947 -- 89,722,210(-) G/A upstream_transcript_variant
rs1000364012 -- 89,718,607(-) G/T 5_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant
rs1000392219 -- 89,709,819(-) G/A coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs1000797349 -- 89,718,309(-) C/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for VPS9D1 Gene

Variant ID Type Subtype PubMed ID
esv2762221 CNV gain+loss 21179565
nsv1057351 CNV loss 25217958
nsv1931 CNV insertion 18451855
nsv428331 CNV gain+loss 18775914
nsv457623 CNV gain 19166990
nsv482951 CNV loss 15286789
nsv509639 CNV insertion 20534489
nsv516241 CNV loss 19592680
nsv573743 CNV gain 21841781
nsv833330 CNV loss 17160897
nsv952079 CNV deletion 24416366

Variation tolerance for VPS9D1 Gene

Residual Variation Intolerance Score: 58.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.07; 50.73% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VPS9D1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VPS9D1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS9D1 Gene

Disorders for VPS9D1 Gene

Additional Disease Information for VPS9D1

No disorders were found for VPS9D1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for VPS9D1 Gene

Publications for VPS9D1 Gene

  1. Isolation and mapping of a putative b subunit of human ATP synthase (ATP-BL) from human leukocytes. (PMID: 10231027) Sugimoto J … Isobe M (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 2 3 4 58
  2. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein MY … Mann M (Cell 2015) 3 58
  3. Toward a confocal subcellular atlas of the human proteome. (PMID: 18029348) Barbe L … Andersson-Svahn H (Molecular & cellular proteomics : MCP 2008) 3 58
  4. Genomic annotation of 15,809 ESTs identified from pooled early gestation human eyes. (PMID: 16368877) Choy KW … Pang CP (Physiological genomics 2006) 3 58
  5. The sequence and analysis of duplication-rich human chromosome 16. (PMID: 15616553) Martin J … Pennacchio LA (Nature 2004) 4 58

Products for VPS9D1 Gene

Sources for VPS9D1 Gene

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